Variable domains Constant domains

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Variable domains Constant domains
(200aa)
(400aa)
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An IgG molecule has several degrees of
conformational flexibility
There is no preferred orientation of the Fab
arms. The Fab arms can move relative both to
each other and to Fc fragment to bind antigens
separated by different distances and in different
orientations. The Fc region can move relative to
the Fab to facilitate interaction with effector
molecules that bind Fc.
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Antigen is recognized by six hypervariables
regions (CDRs, complementary-determining regions)
of antibody light (CDR1 L1, CDR2 L2, CDR3
L3) and heavy chain (CDR1 H1, CDR2 H2, CDR3
H3)
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The picture before this publication (X-ray and
kinetic data)
Lock-and-key mechanism of antibody-antigen
binding (pre-existing-fit or pre-equilibrium)
Antibodies are commonly highly specific
Through shared ligand chemistry or molecular
mimicry
Antibody cross-reactivity
Induced-fit mechanism of binding (proteins
conformational changes upon binding)
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Monoclonal antibody SPE7 (IgE, ?) raised against
a DNP hapten which can also binds several
unrelated compounds with different affinities.
protein Trx-Shear3
Ab2
Ab1
Ab4
furazolidone (Fur, Acenaphthenequinone, C8H5N3O5,
Kd1.2?M),
alizarin red (Az, C14H8O7S, Kd40nM),
2,4-dinitrophenyl (DNP, C6H4N2O5, Kd20nM)
Ab3
Ab3
Ab3
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Conclusion

• Cross-reactivity (or multispecificity) of
  antibody SPE7 is mediated by two modes
• Through a promiscuous, low-affinity pre-existing
  isomer (Ab2) which binds small aromatic haptens
  with low affinity with a subsequent induced-fit
  isomerization that led to the final
  hapten-antibody complexes (Ab3).
• Through preexisting conformational diversity
  enabling SPE7 to bind antigens at either end of
  structural spectrum. This work demonstrates for
  the first time structures of the same antibody
  binding to hapten and protein. Ab4
  (protein-bound) has a long and flat binding site,
  whereas the hapten-bound structures (Ab3) have a
  deep and narrow pocket.

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Conclusion
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Discussion

• It is estimated that we can make 107 - 108
  different antibody molecules. This estimation
  does not take into consideration preexisting
  conformational diversity.